Lots of info here..especially the Border Formalities.
http://www.drivetheamericas.com
Don't leave anything in the car unattended, park in secure guarded hotels at night. Avoid Capitals as best you can.
There is a shuttle between Antigua and Leon Nicaragua, but can't find the info....Nicaragua is worth 5-7 days alone, with a car, try to explore the north, as few get there due to transport time factors...